3/30/2024 0 Comments Xcalibur thermoBackgroundĬonventional DDA performs a survey scan (MS1 scan) on all ions passing through our MS, and then selects the N most intense ions (“Top N”) to analyze sequentially. Targeting in Xcalibur is less powerful, but may be more convenient for some users. MaxQuant.Live ( link to manuscript) is a great alternative to targeted DDA in Xcalibur, but it does require some extra set-up and tuning. Of course SRM/PRM methods are more sensitive, but they’re more limited in the number of proteins analyzed – targeted DDA is a nice middle ground to get what we want and a lot of it too. For single cell proteomics methods ( SCoPE-MS, mPOP) especially, where short methods and long injection times yield at most 10K MS/MS events per experiment, we may need targeting in order to analyze low-abundance pathways of interest. Running data-dependent acquisiton (DDA) mass spectrometry experiments in targeting mode is very powerful and desirable if you are trying to get around the bias towards more intense ions inherent in the data-dependent algorithm.
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